[gmx-users] POPC simulation

[chris.neale at utoronto.ca]

>>   thanks for reply.I want to perform simulation of popc membrane.
>>   Steps which i have done are as follows:
>>   1. download popc128a.pdb, popc.it,lipids.itp
>>   (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies)
>>   2. download ffgmx_lipids files
>>   3.convert POPC of .top & popc.itp into POP as in popc.gro
>>   4. #include "ffgmx.itp"
>>   #include "lipid.itp"
>>   #include "popc.itp"
>>   #include "ffgmxnb.itp"
>>   #include "ffgmxbon.itp"

> These last two lines should already be included in ffgmx.itp, and  
> including them twice may cause some headaches.

I think that the real problem here is exactly as described in the  
error message. There is no POP residue in ffgmx.rtp

>>   ................ in my .top file.
>>
>>   Now when I perform
>>   pdb2gmx -ff gmx -f popc128a.pdb -o popc.gro -p popc.top
>>   it shows the error that"Residue 'POP' not found in residue topology
>> database".
>>   I think that's because of the fact that ffgmx.rtp do not
>>   contain "POP" residue ,but it has DPPC residue.
>>   Plz suggest how can i solve this problem.
>>   thanks.

> Use editconf to convert between .pdb and .gro.  You only need pdb2gmx if you
> don't have a .top file, but Prof. Tieleman has kindly provided this for you
> already, in the form of lipid.itp and popc.itp.

Agreed. There is no need to use pdb2gmx here since you have a popc.itp  
file already. You need to make your own .top file. That shouldn't be  
too difficult. Just look at one you get from pdb2gmx for a protein,  
make the necessary changes, including lipid.itp and putting POP 128 in  
the molecules section at the end (or is it POPC not POP for the  
molecule name? Look at the top of the popc.itp file to see what the  
name of the molecule is.

Chris.